# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 22:40:45 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: (1R,4S,5S,6R)-4-amino-5,6-dihydroxy-2-(hydroxymethyl)cyclohex-2-en-1-yl alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C=C(CO)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 ZD1  ZD1  '(1R,4S,5S,6R)-4-amino-5,6-dihydroxy-2-(hydroxymethyl)cyclohex-2-en-1-yl alpha-D-glucopyranoside'  ligand  46  23  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZD1
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 ZD1  C02  C  CH1   0  -0.136  23.5531  -30.0608  278.0475
 ZD1  C03  C  C1    0  -0.283  24.9322  -30.3277  277.5264
 ZD1  C04  C  C     0   0.073  25.2556  -30.4596  276.2431
 ZD1  C05  C  CH2   0  -0.220  26.6618  -30.7912  275.8361
 ZD1  C07  C  CH1   0   0.002  24.2442  -30.3058  275.1401
 ZD1  C09  C  CH1   0   0.242  23.7953  -31.4485  273.1074
 ZD1  C10  C  CH1   0  -0.017  23.3096  -32.8231  272.6388
 ZD1  C12  C  CH1   0  -0.007  24.4759  -33.7991  272.5695
 ZD1  C14  C  CH1   0   0.040  25.5676  -33.2164  271.6801
 ZD1  C16  C  CH1   0  -0.019  25.9695  -31.8378  272.2022
 ZD1  C17  C  CH2   0  -0.182  27.0005  -31.1297  271.3496
 ZD1  C20  C  CH1   0  -0.010  22.8685  -29.8415  275.6355
 ZD1  C22  C  CH1   0   0.001  22.4951  -30.4175  276.9977
 ZD1  N01  N  NH2   0  -0.819  23.3020  -30.8951  279.2217
 ZD1  O06  O  OH1   0  -0.669  27.1322  -29.8313  274.9117
 ZD1  O08  O  O2    0  -0.503  24.1688  -31.5418  274.4444
 ZD1  O11  O  OH1   0  -0.663  22.3274  -33.3634  273.4832
 ZD1  O13  O  OH1   0  -0.671  24.0924  -35.0337  272.0089
 ZD1  O15  O  OH1   0  -0.672  26.7206  -34.0216  271.6758
 ZD1  O18  O  OH1   0  -0.668  26.5207  -30.9835  270.0350
 ZD1  O19  O  O2    0  -0.499  24.8316  -30.9940  272.2847
 ZD1  O21  O  OH1   0  -0.668  22.9324  -28.4326  275.7051
 ZD1  O23  O  OH1   0  -0.675  22.3664  -31.8091  276.9012
 ZD1  H1   H  HCH1  0   0.241  23.4752  -28.9901  278.2781
 ZD1  H2   H  H     0   0.248  25.7197  -30.4003  278.2731
 ZD1  H3   H  HCH2  0   0.215  26.6755  -31.7967  275.3983
 ZD1  H4   H  HCH2  0   0.217  27.2944  -30.8292  276.7319
 ZD1  H5   H  HCH1  0   0.243  24.6114  -29.5267  274.4596
 ZD1  H6   H  HCH1  0   0.233  22.9929  -30.7100  272.9742
 ZD1  H7   H  HCH1  0   0.224  22.9228  -32.6884  271.6180
 ZD1  H8   H  HCH1  0   0.213  24.8886  -33.9448  273.5794
 ZD1  H9   H  HCH1  0   0.211  25.1575  -33.1092  270.6648
 ZD1  H10  H  HCH1  0   0.236  26.4258  -31.9700  273.1920
 ZD1  H11  H  HCH2  0   0.208  27.9300  -31.7087  271.3877
 ZD1  H12  H  HCH2  0   0.210  27.2146  -30.1588  271.8166
 ZD1  H13  H  HCH1  0   0.232  22.1097  -30.1582  274.9048
 ZD1  H14  H  HCH1  0   0.213  21.5377  -29.9634  277.3086
 ZD1  H15  H  HNH2  0   0.363  24.1034  -30.8924  279.8402
 ZD1  H16  H  HNH2  0   0.359  22.5304  -30.5138  279.7562
 ZD1  H18  H  HOH1  0   0.458  27.8897  -30.2027  274.4502
 ZD1  H19  H  HOH1  0   0.456  21.5005  -32.8924  273.3407
 ZD1  H20  H  HOH1  0   0.452  23.4750  -35.4629  272.6095
 ZD1  H21  H  HOH1  0   0.450  26.4714  -34.8973  271.3632
 ZD1  H22  H  HOH1  0   0.455  27.2185  -30.5919  269.5028
 ZD1  H23  H  HOH1  0   0.452  22.0889  -28.1017  276.0310
 ZD1  H24  H  HOH1  0   0.437  22.5825  -32.1291  277.7941

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 ZD1  O18  C17  single  1.407  0.020  1.407
 ZD1  O15  C14  single  1.406  0.020  1.406
 ZD1  C17  C16  single  1.514  0.020  1.514
 ZD1  C14  C16  single  1.528  0.020  1.528
 ZD1  C14  C12  single  1.524  0.020  1.524
 ZD1  O13  C12  single  1.409  0.020  1.409
 ZD1  C16  O19  single  1.419  0.020  1.419
 ZD1  O19  C09  single  1.399  0.020  1.399
 ZD1  C12  C10  single  1.522  0.020  1.522
 ZD1  C10  C09  single  1.531  0.020  1.531
 ZD1  C10  O11  single  1.403  0.020  1.403
 ZD1  C09  O08  single  1.391  0.020  1.391
 ZD1  O08  C07  single  1.420  0.020  1.420
 ZD1  C07  C20  single  1.534  0.020  1.534
 ZD1  C07  C04  single  1.504  0.020  1.504
 ZD1  O06  C05  single  1.413  0.020  1.413
 ZD1  C20  O21  single  1.412  0.020  1.412
 ZD1  C20  C22  single  1.525  0.020  1.525
 ZD1  C05  C04  single  1.501  0.020  1.501
 ZD1  C04  C03  double  1.330  0.020  1.330
 ZD1  O23  C22  single  1.401  0.020  1.401
 ZD1  C22  C02  single  1.533  0.020  1.533
 ZD1  C03  C02  single  1.498  0.020  1.498
 ZD1  C02  N01  single  1.462  0.020  1.462
 ZD1  C02  H1   single  0.970  0.020  1.090
 ZD1  C03  H2   single  0.930  0.020  1.080
 ZD1  C05  H3   single  0.970  0.020  1.090
 ZD1  C05  H4   single  0.970  0.020  1.090
 ZD1  C07  H5   single  0.970  0.020  1.090
 ZD1  C09  H6   single  0.970  0.020  1.090
 ZD1  C10  H7   single  0.970  0.020  1.090
 ZD1  C12  H8   single  0.970  0.020  1.090
 ZD1  C14  H9   single  0.970  0.020  1.090
 ZD1  C16  H10  single  0.970  0.020  1.090
 ZD1  C17  H11  single  0.970  0.020  1.090
 ZD1  C17  H12  single  0.970  0.020  1.090
 ZD1  C20  H13  single  0.970  0.020  1.090
 ZD1  C22  H14  single  0.970  0.020  1.090
 ZD1  N01  H15  single  0.890  0.020  1.040
 ZD1  N01  H16  single  0.890  0.020  1.040
 ZD1  O06  H18  single  0.850  0.020  0.980
 ZD1  O11  H19  single  0.850  0.020  0.980
 ZD1  O13  H20  single  0.850  0.020  0.980
 ZD1  O15  H21  single  0.850  0.020  0.980
 ZD1  O18  H22  single  0.850  0.020  0.980
 ZD1  O21  H23  single  0.850  0.020  0.980
 ZD1  O23  H24  single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 ZD1  H1   C02  N01  112.06  3.000
 ZD1  H1   C02  C22  108.78  3.000
 ZD1  N01  C02  C22  107.38  3.000
 ZD1  H1   C02  C03  108.19  3.000
 ZD1  N01  C02  C03  109.62  3.000
 ZD1  C22  C02  C03  110.84  3.000
 ZD1  H2   C03  C04  118.67  3.000
 ZD1  H2   C03  C02  116.08  3.000
 ZD1  C04  C03  C02  125.25  3.000
 ZD1  C07  C04  C05  116.98  3.000
 ZD1  C05  C04  C03  120.75  3.000
 ZD1  C07  C04  C03  122.26  3.000
 ZD1  H4   C05  H3   106.68  3.000
 ZD1  H4   C05  O06  111.45  3.000
 ZD1  H3   C05  O06  110.95  3.000
 ZD1  H4   C05  C04  109.05  3.000
 ZD1  H3   C05  C04  108.81  3.000
 ZD1  O06  C05  C04  109.82  3.000
 ZD1  H5   C07  O08  109.37  3.000
 ZD1  H5   C07  C20  106.58  3.000
 ZD1  O08  C07  C20  111.96  3.000
 ZD1  H5   C07  C04  107.59  3.000
 ZD1  C20  C07  C04  113.40  3.000
 ZD1  O08  C07  C04  107.81  3.000
 ZD1  H6   C09  O19  104.55  3.000
 ZD1  H6   C09  O08  110.96  3.000
 ZD1  O19  C09  O08  112.83  3.000
 ZD1  H6   C09  C10  109.56  3.000
 ZD1  O08  C09  C10  108.61  3.000
 ZD1  O19  C09  C10  110.28  3.000
 ZD1  H7   C10  O11  111.06  3.000
 ZD1  H7   C10  C12  107.80  3.000
 ZD1  O11  C10  C12  108.47  3.000
 ZD1  H7   C10  C09  106.59  3.000
 ZD1  O11  C10  C09  112.55  3.000
 ZD1  C12  C10  C09  110.27  3.000
 ZD1  H8   C12  O13  110.56  3.000
 ZD1  H8   C12  C14  108.51  3.000
 ZD1  O13  C12  C14  107.32  3.000
 ZD1  H8   C12  C10  109.29  3.000
 ZD1  O13  C12  C10  111.80  3.000
 ZD1  C14  C12  C10  109.28  3.000
 ZD1  H9   C14  O15  111.01  3.000
 ZD1  H9   C14  C16  108.99  3.000
 ZD1  O15  C14  C16  107.57  3.000
 ZD1  H9   C14  C12  107.99  3.000
 ZD1  C16  C14  C12  109.51  3.000
 ZD1  O15  C14  C12  111.73  3.000
 ZD1  H10  C16  O19  110.63  3.000
 ZD1  H10  C16  C17  106.32  3.000
 ZD1  O19  C16  C17  107.50  3.000
 ZD1  H10  C16  C14  107.99  3.000
 ZD1  O19  C16  C14  110.21  3.000
 ZD1  C17  C16  C14  114.13  3.000
 ZD1  H12  C17  H11  106.68  3.000
 ZD1  H12  C17  O18  111.83  3.000
 ZD1  H11  C17  O18  112.12  3.000
 ZD1  H12  C17  C16  107.86  3.000
 ZD1  H11  C17  C16  108.12  3.000
 ZD1  O18  C17  C16  110.04  3.000
 ZD1  H13  C20  O21  110.56  3.000
 ZD1  H13  C20  C22  108.40  3.000
 ZD1  O21  C20  C22  110.11  3.000
 ZD1  H13  C20  C07  108.48  3.000
 ZD1  C22  C20  C07  113.18  3.000
 ZD1  O21  C20  C07  106.10  3.000
 ZD1  H14  C22  O23  110.38  3.000
 ZD1  H14  C22  C20  107.96  3.000
 ZD1  O23  C22  C20  109.63  3.000
 ZD1  H14  C22  C02  108.06  3.000
 ZD1  O23  C22  C02  109.99  3.000
 ZD1  C20  C22  C02  110.78  3.000
 ZD1  H16  N01  H15  106.24  3.000
 ZD1  H16  N01  C02  109.86  3.000
 ZD1  H15  N01  C02  110.68  3.000
 ZD1  H18  O06  C05  108.28  3.000
 ZD1  C09  O08  C07  115.25  3.000
 ZD1  H19  O11  C10  108.90  3.000
 ZD1  H20  O13  C12  108.49  3.000
 ZD1  H21  O15  C14  108.03  3.000
 ZD1  H22  O18  C17  108.19  3.000
 ZD1  C16  O19  C09  115.79  3.000
 ZD1  H23  O21  C20  108.66  3.000
 ZD1  H24  O23  C22  104.06  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 ZD1  Var_01  C07  C04  C03  C02     2.07  30.0  1
 ZD1  Var_02  O06  C05  C04  C03  -125.66  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 ZD1  chir_01  C02  C22  C03  N01  positiv
 ZD1  chir_02  C07  O08  C20  C04  negativ
 ZD1  chir_03  C09  O19  O08  C10  positiv
 ZD1  chir_04  C10  O11  C09  C12  negativ
 ZD1  chir_05  C12  O13  C10  C14  positiv
 ZD1  chir_06  C14  O15  C12  C16  negativ
 ZD1  chir_07  C16  O19  C14  C17  negativ
 ZD1  chir_08  C20  O21  C07  C22  negativ
 ZD1  chir_09  C22  O23  C20  C02  positiv

